diff --git a/NEWS.md b/NEWS.md
index 17d92ed88803e7acc6ce12a90ad2489bbb89efba..de153a815c687791560c69278e7ea5f0ddc89efa 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,8 +1,9 @@
# stressaddition 3.0.0
-* Rename all instances of "effect" to "survival".
-* Rename all instances of "ec" to "lc".
-* Rename `predict_mixture()` to `multi_tox()`.
+* Renamed all instances of "effect" to "survival".
+* Renamed all instances of "ec" to "lc".
+* Renamed `predict_mixture()` to `multi_tox()`.
+* The argument `proportion_ca` in the mixture model `multi_tox` was renamed and its value reversed. It is now called `sa_contribution` and specifies the proportion of stress addition in the calculation of toxicant stress. To convert your code from the old version use this equation: sa_contribution = 1 - proportion_ca.
# stressaddition 2.7.0
diff --git a/R/multi_tox.R b/R/multi_tox.R
index 3a9bab1f164e7761b88a3f03e75d426ad79ab2c1..84a75a6191ba749316eb65d8d9c45fdcbb69a2a1 100644
--- a/R/multi_tox.R
+++ b/R/multi_tox.R
@@ -34,8 +34,9 @@
#' the mixture. Both vectors must either be the same length or the longer
#' length must be a multiple of the shorter length. That's because the shorter
#' concentration vector gets recycled to the length of the longer one.
-#' @param proportion_ca The proportion of concentration addition in the
-#' calculation of the toxicant stress of the mixture. Must be between 0 and 1.
+#' @param sa_contribution The proportion of stress addition contributing to the
+#' calculation of the toxicant stress in the mixture. Must be between 0 and 1
+#' where 1 stands for 100 \% stress addition.
#' @param survival_max Controls the scaling of the result. This represents the
#' maximum value the survival could possibly reach. For survival data in
#' percent this should be 100 (the default).
@@ -64,9 +65,9 @@
#' # Example of symmetric prediction:
#' conc_a <- c(0, 0.03, 0.3, 3)
#' conc_b <- 5.5
-#' prop_ca <- 0.75
-#' mix_a <- multi_tox(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca)
-#' mix_b <- multi_tox(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca)
+#' sa_contrib <- 0.75
+#' mix_a <- multi_tox(toxicant_a , toxicant_b , conc_a, conc_b, sa_contrib)
+#' mix_b <- multi_tox(toxicant_b , toxicant_a , conc_b, conc_a, sa_contrib)
#' identical(mix_a$survival, mix_b$survival)
#'
#' @export
@@ -74,7 +75,7 @@ multi_tox <- function(model_a,
model_b,
concentration_a,
concentration_b,
- proportion_ca = 0.5,
+ sa_contribution = 0.5,
survival_max = 100) {
stopifnot(
inherits(model_a, "ecxsys"),
@@ -85,8 +86,8 @@ multi_tox <- function(model_a,
length(concentration_b) > 0,
all(!is.na(concentration_a)),
all(!is.na(concentration_b)),
- proportion_ca >= 0,
- proportion_ca <= 1,
+ sa_contribution >= 0,
+ sa_contribution <= 1,
model_a$args$p == model_b$args$p,
model_a$args$q == model_b$args$q
)
@@ -127,8 +128,8 @@ multi_tox <- function(model_a,
sys_total <- (sys_a + sys_b) / 2
# combined stress and result ------------------------------------------
- proportion_sam <- 1 - proportion_ca
- stress_tox_total <- stress_tox_ca * proportion_ca + stress_tox_sam * proportion_sam
+ ca_contribution <- 1 - sa_contribution
+ stress_tox_total <- stress_tox_sam * sa_contribution + stress_tox_ca * ca_contribution
stress_total <- stress_tox_total + sys_total
survival <- stress_to_survival(stress_total) * survival_max
diff --git a/man/multi_tox.Rd b/man/multi_tox.Rd
index f518529eeab8103140c199db26eb9529f74057ff..62ecbddc9e424ce5eb85053fbd5574b183d922ed 100644
--- a/man/multi_tox.Rd
+++ b/man/multi_tox.Rd
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/predict_mixture.R
+% Please edit documentation in R/multi_tox.R
\name{multi_tox}
\alias{multi_tox}
\title{Predict the survival of a mixture of two toxicants}
@@ -9,7 +9,7 @@ multi_tox(
model_b,
concentration_a,
concentration_b,
- proportion_ca = 0.5,
+ sa_contribution = 0.5,
survival_max = 100
)
}
@@ -21,8 +21,9 @@ the mixture. Both vectors must either be the same length or the longer
length must be a multiple of the shorter length. That's because the shorter
concentration vector gets recycled to the length of the longer one.}
-\item{proportion_ca}{The proportion of concentration addition in the
-calculation of the toxicant stress of the mixture. Must be between 0 and 1.}
+\item{sa_contribution}{The proportion of stress addition contributing to the
+calculation of the toxicant stress in the mixture. Must be between 0 and 1
+where 1 stands for 100 \% stress addition.}
\item{survival_max}{Controls the scaling of the result. This represents the
maximum value the survival could possibly reach. For survival data in
@@ -66,9 +67,9 @@ multi_tox(
# Example of symmetric prediction:
conc_a <- c(0, 0.03, 0.3, 3)
conc_b <- 5.5
-prop_ca <- 0.75
-mix_a <- multi_tox(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca)
-mix_b <- multi_tox(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca)
+sa_contrib <- 0.75
+mix_a <- multi_tox(toxicant_a , toxicant_b , conc_a, conc_b, sa_contrib)
+mix_b <- multi_tox(toxicant_b , toxicant_a , conc_b, conc_a, sa_contrib)
identical(mix_a$survival, mix_b$survival)
}
diff --git a/tests/testthat/test-multi_tox.R b/tests/testthat/test-multi_tox.R
index 77bf217d5bbb61c87ce08577f3b516a3840cde5b..d1fd5524c72fb153635dcf758e10b29ed0ed5a19 100644
--- a/tests/testthat/test-multi_tox.R
+++ b/tests/testthat/test-multi_tox.R
@@ -39,7 +39,7 @@ test_that("results have not changed", {
model_b,
c(0, 0.01, 0.1, 1, 7, 15),
5,
- 0.3
+ 0.7
)
reference <- data.frame(
concentration_a = c(0, 0.01, 0.1, 1, 7, 15),
@@ -59,7 +59,7 @@ test_that("results have not changed", {
model_b,
c(0, 0.01, 0.1, 1, 7, 15),
c(0, 0.02, 0.2, 2, 14, 30),
- 0.3
+ 0.7
)
reference <- data.frame(
concentration_a = c(0, 0.01, 0.1, 1, 7, 15),
@@ -79,7 +79,7 @@ test_that("results have not changed", {
model_b,
c(0, 0.01, 0.1, 1, 7, 15),
c(0, 0.02, 0.2, 2, 14, 30),
- 0.3,
+ 0.7,
42
)
reference <- data.frame(
@@ -99,9 +99,9 @@ test_that("results have not changed", {
test_that("predictions are symmetric", {
conc_a <- c(0, 10^seq(log10(0.001), log10(40), length.out = 50))
conc_b <- 3.5
- prop_ca <- 0.8
- survival_12 <- multi_tox(model_a, model_b, conc_a, conc_b, prop_ca)$survival
- survival_21 <- multi_tox(model_b, model_a, conc_b, conc_a, prop_ca)$survival
+ sa_contrib <- 0.8
+ survival_12 <- multi_tox(model_a, model_b, conc_a, conc_b, sa_contrib)$survival
+ survival_21 <- multi_tox(model_b, model_a, conc_b, conc_a, sa_contrib)$survival
expect_equal(survival_12, survival_21)
})